Population genomic analysis of gut microbial colonization in premature infants

早产儿肠道微生物定植的群体基因组分析

基本信息

批准号：
8495896
负责人：
Jillian Banfield
金额：
$ 72.22万
依托单位：
UNIVERSITY OF CALIFORNIA BERKELEY
依托单位国家：
美国
项目类别：
财政年份：
2011
资助国家：
美国
起止时间：
2011-07-15 至 2016-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8495896
关键词：
Acids Bacteriophages Beryllium Birth Communities Community Developments DNA DNA Insertion Elements Data Development Disease Drainage procedure Ecology Ecosystem Elements Emergency Situation Environment Evolution Feces Gastrointestinal tract structure Genes Genetic Genetic Heterogeneity Genome Genomics Health Heterogeneity Human Human body Immigration In Situ Individual Infant Infant Development Intestines Life Mediating Metabolic Metagenomics Methods Microbe Mining Necrotizing Enterocolitis Neonatal Newborn Infant Onset of illness Organism Outcome Pathogenesis Pattern Phase Phenotype Phylogenetic Analysis Plasmids Play Population Population Analysis Population Dynamics Population Heterogeneity Predatory Behavior Premature Infant Process Research Resolution Ribosomal RNA Role Sampling Series Shapes Source Structure System Testing Time Translating Variant Virulent Work disorder prevention gastrointestinal gastrointestinal system improved member metagenomic sequencing microbial microbial colonization microbial community migration neonate next generation sequencing premature rRNA Genes virus host interaction

项目摘要

DESCRIPTION (provided by applicant): Microbial communities associated with the human body, in particular the gastrointestinal tract, play crucial roles in health and disease. The objective of this proposal is to understand how specific patterns in gut microbial succession are related to health and disease, and specifically to neonatal necrotizing enterocolitis (NEC). Although available evidence suggests that intestinal microbes contribute to the pathogenesis of NEC, the details of this relationship remain poorly understood. At present, relatively little is known about the gut colonization process in premature newborns, and about differences between this process in premature infants with and without NEC. We propose complementary high-throughput phylogenetic and metagenomic analyses to study microbial colonization of the premature infant gut during the first three weeks after birth. Our proposed work will elucidate, at high resolution, the population structure of microbial communities that develop during colonization of the premature infant gut and examine the roles of early colonists, gastrointestinal tract-mediated selection, immigration, the effects of mobile elements on genomic variation and microbial survival, and examine how these processes relate to onset of NEC. We will use "next-generation" sequencing to resolve species- and population-level community succession patterns during the critical initial period of gut colonization in babies that do and do not go on to develop NEC. We will profile community development using high-throughput 16S rRNA tag sequencing of stool samples collected daily during the first three weeks after birth. We will then carry out deep metagenomic sequencing of microbial DNA from half of these fecal time series samples to reconstruct genomes for coexisting bacterial, archaeal, phage, and plasmid populations. This will allow us to track species membership, community structure, metabolic potential, and population-level genetic heterogeneity. We will use these data to test the extent to which initial consortia predict succeeding community diversity [Aim 1], the importance of in situ diversification mediated by phage, insertion elements, and plasmids vs. immigration in determining population structure and metabolic potential [Aim 2], and to define ecological trajectories that correlate with health and disease [Aim 3]. Our preliminary metagenomic data conclusively demonstrate that the proposed approach can be used to reconstruct near-complete genomes of coexisting organisms from premature infant gut fecal samples with sufficient population depth to analyze population heterogeneity and dynamics. Improved understanding of the colonization process in the premature infant gut could translate to improved outcomes for premature babies by suggesting more effective strategies for disease prevention and treatment. More broadly, this research will uncover aspects of ecosystem colonization dynamics that have implications for other aspects of human health and the environment. !

描述（由申请人提供）：与人体相关的微生物群落，特别是胃肠道，在健康和疾病中发挥着至关重要的作用。该提案的目的是了解肠道微生物演替的特定模式如何与健康和疾病相关，特别是与新生儿坏死性小肠结肠炎（NEC）相关。尽管现有证据表明肠道微生物有助于 NEC 的发病机制，但这种关系的细节仍然知之甚少。目前，人们对早产儿肠道定植过程以及患有和不患有 NEC 的早产儿肠道定植过程的差异知之甚少。我们提出互补的高通量系统发育和宏基因组分析来研究早产儿出生后前三周内肠道的微生物定植。我们提出的工作将以高分辨率阐明早产儿肠道定植过程中形成的微生物群落的种群结构，并检查早期定殖者的作用、胃肠道介导的选择、迁移、移动元件对基因组变异的影响和微生物的存活，并检查这些过程与 NEC 的发生有何关系。我们将使用“下一代”测序来解决发生和未发生 NEC 的婴儿肠道定植关键初始阶段的物种和种群水平的群落演替模式。我们将使用高通量 16S rRNA 标签测序对出生后前三周内每天收集的粪便样本进行群落发展分析。然后，我们将对一半粪便时间序列样本中的微生物 DNA 进行深度宏基因组测序，以重建共存细菌、古菌、噬菌体和质粒群体的基因组。这将使我们能够跟踪物种成员、群落结构、代谢潜力和种群水平的遗传异质性。我们将使用这些数据来测试初始联盟预测后续群落多样性的程度[目标 1]，噬菌体、插入元件和质粒介导的原位多样化与迁移在确定种群结构和代谢潜力方面的重要性[目标 2] ]，并定义与健康和疾病相关的生态轨迹[目标 3]。我们的初步宏基因组数据最终证明，所提出的方法可用于从具有足够种群深度的早产儿肠道粪便样本中重建共存生物体的近乎完整的基因组，以分析种群异质性和动态。提高对早产儿肠道定植过程的了解可以通过提出更有效的疾病预防和治疗策略来改善早产儿的结局。更广泛地说，这项研究将揭示生态系统殖民动态的各个方面，这些方面对人类健康和环境的其他方面产生影响。！